The genome sequence of the thickback sole, Microchirus variegatus (Donovan, 1808)

We present a genome assembly from an individual female Microchirus variegatus (the thickback sole; Chordata; Actinopteri; Pleuronectiformes; Soleidae). The genome sequence is 724.7 megabases in span. Most of the assembly is scaffolded into 23 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 17.42 kilobases in length.


Background
Microchirus variegatus (Donovan et al., 1802), also known as the thickback sole or lucky sole, is a flatfish belonging to the Soleidae family.It is distributed in the north-east Atlantic Ocean and the Mediterranean Sea (Amara et al., 1998;Tous et al., 2015).The thickback sole has a slender and elongated oval body shape, but is thicker from side to side.The thickback sole is among the smaller-sized sole species, typically measuring 12 to 15 cm, but can reach up to 20 cm for the older age classes of 10 to 13 years old (Déniel, 1981).Spawning occurs in springtime, and unlike common soles, the juveniles of thickback soles settle offshore and then migrate inshore (Amara et al., 1998).The thickback sole species is benthic and can be located on sea-beds consisting of sand and mud, with a preference for coarse sand.It feeds on a wide range of small benthic organisms, mainly crustaceans such as amphipods and shrimp, as well as polychaetes and bivalves.
Less commercially valuable than other flatfish species (Machado et al., 2020), M. varigatus is currently listed as of least concern by the IUCN red list and is a somewhat common species in its given distributions (Tous et al., 2015).This chromosome-level reference genome for Microchirus variegatus is the first for this species, and will provide the tools for further study into this species.

Genome sequence report
The genome was sequenced from one female Microchirus variegatus (Figure 1) collected from RV MBA Sepia (50.25,.A total of 36-fold coverage in Pacific Biosciences single-molecule HiFi long reads was generated.Primary assembly contigs were scaffolded with chromosome conformation Hi-C data.Manual assembly curation corrected 22 missing joins or mis-joins, reducing the scaffold number by 3.59%. The final assembly has a total length of 724.7 Mb in 187 sequence scaffolds with a scaffold N50 of 29.8 Mb (Table 1).The snail plot in Figure 2 provides a summary of the assembly statistics, while the distribution of assembly scaffolds on GC proportion and coverage is shown in Figure 3.The cumulative assembly plot in Figure 4 shows curves for subsets of scaffolds assigned to different phyla.Most (95.61%) of the assembly sequence was assigned to 23 chromosomal-level scaffolds.Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size (Figure 5; Table 2).While not fully phased, the assembly deposited is of one haplotype.Contigs corresponding to the second haplotype have also been deposited.The mitochondrial genome was also assembled and can be found as a contig within the multifasta file of the genome submission.

Sample acquisition and nucleic acid extraction
A female Microchirus variegatus (specimen ID MBA-210611-004A, ToLID fMicVar1) was taken using an Agassiz trawl deployed from RV MBA Sepia (latitude 50.25, longitude -4.22) on 2021-06-11.The collectors were Rob Mrowicki, Patrick Adkins, Joanna Harley and Rachel Brittain (Marine Biological Association).The specimen was identified by Rachel Brittain, based on gross morphology and DNA barcoding.Samples taken from the animal were preserved in liquid nitrogen.The fish was first anaesthetised and then overdosed using Aquased (2-phenoxyethanol).Destruction of the brain was used as a secondary method to ensure the animal was deceased before tissue sampling took place as in accordance with Schedule 1 methodology under the home office licence.Samples taken from the animal were preserved on dry ice.In sample preparation, the fMicVar1 sample was weighed and dissected on dry ice (Jay et al., 2023).For sample homogenisation, muscle tissue was cryogenically disrupted using the Covaris cryoPREP ® Automated Dry Pulverizer       (Zhou et al., 2023).The assembly was checked for contamination and corrected using the gEVAL system (Chow et al., 2016) as described previously (Howe et al., 2021).Manual curation was performed using gEVAL, HiGlass (Kerpedjiev et al., 2018) andPretextView (Harry, 2022).The mitochondrial genome was assembled using MitoHiFi (Uliano-Silva et al., 2023), which runs MitoFinder (Allio et al., 2020) or MITOS (Bernt et al., 2013) and uses these annotations to select the final mitochondrial contig and to ensure the general quality of the sequence.
The genome was analysed within the BlobToolKit environment (Challis et al., 2020) andBUSCO scores (Manni et al., 2021;Simão et al., 2015) were calculated.Further, the Wellcome Sanger Institute employs a process whereby due diligence is carried out proportionate to the nature of the materials themselves, and the circumstances under which they have been/are to be collected and provided for use.The purpose of this is to address and mitigate any potential legal and/or ethical implications of receipt and use of the materials as part of the research project, and to ensure that in doing so we align with best practice wherever possible.The overarching areas of consideration are: • Ethical review of provenance and sourcing of the material

Jianguo Lu
Zhuhai Campus, Sun Yat-Sen University, Tangjiawan, China The manuscript titled "The genome sequence of the thickback sole, Microchirus variegatus (Donovan, 1808)" presents a comprehensive genomic assembly from an individual female specimen of this lesser-known flatfish species.Spanning 724.7 megabases, the assembly is meticulously organized into 23 chromosomal pseudomolecules, reflecting a commendable effort in achieving high-resolution genomic structure elucidation.Additionally, the inclusion of the 17.42kilobase mitochondrial genome underscores the completeness of the presented dataset.The methodology is suitable and overall, very well described.I have noticed only few small inconsistencies: Table 1 of the manuscript lists the Genome Assembly with a 'Number of contigs' as 642 for the accession GCA_963457635.1.However, the same accession on NCBI database cites a count of 641 contigs.Please reconcile this discrepancy and confirm the accurate number of contigs in the assembly. 1.
In the data note, while the full name 'Marine Biological Association' is correctly presented in the author affiliation details, its initial appearance in the main body of the text omits the expansion from the abbreviation 'MBA'.This omission has the potential to cause confusion for readers unfamiliar with the acronym.Hence, it is recommended to introduce the full designation 'Marine Biological Association (MBA)' at its first use in the text to promote clarity and accessibility.

2.
The same data in the manuscript does not use the same decimal intensive reading.Table 1 cites the 'Span (Mb)' as 724.7, whereas Figure 2 mentions 725 megabases.Harmonizing these figures to a consistent level of precision throughout would contribute to a smoother reading experience and ensure absolute clarity.While this adjustment is not a strict necessity, implementing it could refine the manuscript's overall coherence.

3.
The 'Genome assembly, curation, and evaluation' phase encompassed a suite of software tools.While Table 3 provides version details and source links for several of these tools, there appears to be an omission regarding others instrumental in the process.

4.
Is the rationale for creating the dataset(s) clearly described?It is an excellent piece of research that is carefully carried out.The reported genome assembly at the chromosome level is of high quality as shown by the BUSCO values.The sequencing coverage is also good.I just need some clarification.
1. Is there any information regarding genome size of Microchirus variegatus estimated using flow cytometry?If yes, then what percentage of genome has been covered in this assembly?2. It will be good if you can give details regarding the repeat content of the genome and the major repeat units represented in the genome.I would recommend accepting this paper after addressing these comments.
Is the rationale for creating the dataset(s) clearly described?Yes

Are the protocols appropriate and is the work technically sound? Yes
Are sufficient details of methods and materials provided to allow replication by others?

Yes
Are the datasets clearly presented in a useable and accessible format?Yes Competing Interests: No competing interests were disclosed.
Reviewer Expertise: Fish genetics and genomics I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.

Figure 1 .
Figure 1.Photographs of the Microchirus variegatus (fMicVar1) specimen used for genome sequencing: a) View of the right side of the whole animal, b) View of the head of the right side of the animal, c) View of the left side of the whole animal, d) View of the head of the left side of the animal.

Figure 2 .
Figure 2. Genome assembly of Microchirus variegatus, fMicVar1.1:metrics.The BlobToolKit snail plot shows N50 metrics and BUSCO gene completeness.The main plot is divided into 1,000 size-ordered bins around the circumference with each bin representing 0.1% of the 724,694,306 bp assembly.The distribution of scaffold lengths is shown in dark grey with the plot radius scaled to the longest scaffold present in the assembly (47,546,321 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (29,835,075 and 20,522,917 bp), respectively.The pale grey spiral shows the cumulative scaffold count on a log scale with white scale lines showing successive orders of magnitude.The blue and pale-blue area around the outside of the plot shows the distribution of GC, AT and N percentages in the same bins as the inner plot.A summary of complete, fragmented, duplicated and missing BUSCO genes in the actinopterygii_odb10 set is shown in the top right.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/CAUOPW01/dataset/CAUOPW01/snail.

Figure 3 .
Figure 3. Genome assembly of Microchirus variegatus, fMicVar1.1:BlobToolKit GC-coverage plot.Sequences are coloured by phylum.Circles are sized in proportion to sequence length.Histograms show the distribution of sequence length sum along each axis.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/CAUOPW01/dataset/CAUOPW01/blob.

Figure 4 .
Figure 4. Genome assembly of Microchirus variegatus, fMicVar1.1:BlobToolKit cumulative sequence plot.The grey line shows cumulative length for all sequences.Coloured lines show cumulative lengths of sequences assigned to each phylum using the buscogenes taxrule.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/CAUOPW01/dataset/CAUOPW01/cumulative.

Figure 5 .
Figure 5. Genome assembly of Microchirus variegatus, fMicVar1.1:Hi-C contact map of the fMicVar1.1 assembly, visualised using HiGlass.Chromosomes are shown in order of size from left to right and top to bottom.An interactive version of this figure may be viewed at https://genome-note-higlass.tol.sanger.ac.uk/l/?d=NshZEA2dQ8e4VXrq_Qlgow.

©
2024 Sukumaran S. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Sandhya Sukumaran ICAR-Central Marine Fisheries Research Institute, Kochi, India Title of the paper : The genome sequence of the thickback sole, Microchirus variegatus (Donovan, 1808) The article describes the whole genome sequencing of the thickback sole, Microchirus variegatus.

Darwin Tree of Life Project Sampling Code of Practice', which
can be found in full on the Darwin Tree of Life website here.By agreeing with and signing up to the Sampling Code of Practice, the Darwin Tree of Life Partner agrees they will meet the legal and ethical requirements and standards set out within this document in respect of all samples acquired for, and supplied to, the Darwin Tree of Life Project.

Open Peer Review Current Peer Review Status: Version 1
This is an open access peer review report distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.
https://doi.org/10.21956/wellcomeopenres.23383.r82288